Variant ID: vg0401302211 (JBrowse) | Variation Type: SNP |
Chromosome: chr04 | Position: 1302211 |
Reference Allele: C | Alternative Allele: T |
Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 66. )
TGAAGTGCAAAGGGACATGTTCTCACATCAATCGCATGCAAGGTATATGCATTGTTGTAATTGTGATGCTGAAGGCACTGCTCACAAATCCTACATTATT[C/T]
AGCAGCACCACACAACAAGGAACTAGGCAAATTTAGTACAAGTTCAAGCCAAGTAAACTATCTGTCAATTTGGTCCGTAGAAAACATGGTTTGTTTAGTT
AACTAAACAAACCATGTTTTCTACGGACCAAATTGACAGATAGTTTACTTGGCTTGAACTTGTACTAAATTTGCCTAGTTCCTTGTTGTGTGGTGCTGCT[G/A]
AATAATGTAGGATTTGTGAGCAGTGCCTTCAGCATCACAATTACAACAATGCATATACCTTGCATGCGATTGATGTGAGAACATGTCCCTTTGCACTTCA
Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 43.80% | 4.50% | 0.68% | 51.02% | NA |
All Indica | 2759 | 37.60% | 7.50% | 0.83% | 54.11% | NA |
All Japonica | 1512 | 62.40% | 0.30% | 0.53% | 36.77% | NA |
Aus | 269 | 8.60% | 0.00% | 0.00% | 91.45% | NA |
Indica I | 595 | 71.40% | 0.30% | 1.01% | 27.23% | NA |
Indica II | 465 | 24.50% | 17.60% | 1.72% | 56.13% | NA |
Indica III | 913 | 26.10% | 10.10% | 0.22% | 63.64% | NA |
Indica Intermediate | 786 | 33.10% | 3.80% | 0.89% | 62.21% | NA |
Temperate Japonica | 767 | 56.30% | 0.00% | 0.91% | 42.76% | NA |
Tropical Japonica | 504 | 64.30% | 0.20% | 0.20% | 35.32% | NA |
Japonica Intermediate | 241 | 78.00% | 1.20% | 0.00% | 20.75% | NA |
VI/Aromatic | 96 | 20.80% | 0.00% | 0.00% | 79.17% | NA |
Intermediate | 90 | 48.90% | 5.60% | 1.11% | 44.44% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0401302211 | C -> DEL | N | N | silent_mutation | Average:19.602; most accessible tissue: Callus, score: 78.374 | N | N | N | N |
vg0401302211 | C -> T | LOC_Os04g03120.1 | upstream_gene_variant ; 1685.0bp to feature; MODIFIER | silent_mutation | Average:19.602; most accessible tissue: Callus, score: 78.374 | N | N | N | N |
vg0401302211 | C -> T | LOC_Os04g03140.1 | downstream_gene_variant ; 4122.0bp to feature; MODIFIER | silent_mutation | Average:19.602; most accessible tissue: Callus, score: 78.374 | N | N | N | N |
vg0401302211 | C -> T | LOC_Os04g03130.1 | intron_variant ; MODIFIER | silent_mutation | Average:19.602; most accessible tissue: Callus, score: 78.374 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0401302211 | NA | 9.85E-06 | mr1632 | Ind_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
vg0401302211 | NA | 2.48E-06 | mr1040_2 | Ind_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
vg0401302211 | 7.36E-07 | 9.29E-09 | mr1362_2 | Ind_All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
vg0401302211 | NA | 2.68E-07 | mr1836_2 | Ind_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |